SUNY at Albany
June 19-23, 2001
Approximate Dynamics of DNA, the 11 nm and 30 nm fibers
It is well known that a hierarchy of folded structures exists that enables DNA to be neatly compacted into the nucleus. The folding also defines a hierarchy of time and energy scales affecting the dynamics of DNA. An elastic rod model is used to describe this interrelation of structure and dynamics. In particular elastic constants (Young and Shear modulus, torsional rigidity and bending stiffness) for the 11nm and 30nm fibers have been obtained based on elastic properties for linear DNA and assuming a given fold geometry. Alternatively, the elastic constants for each fiber can be taken directly from experimental data. Clearly the simplified model, presented here, of the 11nm and 30nm fibers will not likely yield accurate results since the affects of histones have not been included. However, comparison of differences between this simple model and experimental results will shed light on the role of the histones in affecting the structure and dynamics of these fibers.
This approach can be utilized to predict static and dynamic properties of each folded state. The propagation of linear waves that excite an extension, twist, bend or shear in the 11nm and 30nm fibers were studied. In particular, the velocity of extension waves in linear DNA is approximately 8.2A/ps. In the 11nm fiber it is approximately 8.5A/ns, three orders of magnitude slower than in linear DNA. In the30nm fiber it is approximately 12.7A/ns. The hierarchy of folding thus enables molecular interactions at the atomic level, such as those that occur between zinc-fingers and DNA, to be directly integrated into multi-molecular complexes at the level of the 11nm and 30nm fibers that orchestrate larger-scale biological processes. In this manner DNA serves not just the passive role of the genetic code, but it also provides a channel for proteins, that are not in direct contact, to transmit and actively process mechanical signals to one another.
Thomas C. Bishop and Oleksandr O. Zhmudsky
Center for Bioenvironmental Research at Tulane and Xavier Universities, 1430 Tulane Avenue, New Orleans, LA 70112.